GeneBe

1-47389707-C-G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000699074.1(CMPK1):​c.550-4574C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000074 ( 0 hom., cov: 20)

Consequence

CMPK1
ENST00000699074.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Publications

3 publications found
Variant links:
Genes affected
CMPK1 (HGNC:18170): (cytidine/uridine monophosphate kinase 1) This gene encodes one of the enzymes required for cellular nucleic acid biosynthesis. This enzyme catalyzes the transfer of a phosphate group from ATP to CMP, UMP, or dCMP, to form the corresponding diphosphate nucleotide. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Feb 2012]
LINC01389 (HGNC:50661): (long intergenic non-protein coding RNA 1389)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC01389NR_126355.1 linkn.405-3351G>C intron_variant Intron 3 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CMPK1ENST00000699074.1 linkc.550-4574C>G intron_variant Intron 5 of 5 ENSP00000514113.1 A0A8V8TMN5
LINC01389ENST00000420876.1 linkn.159-3351G>C intron_variant Intron 1 of 2 3
LINC01389ENST00000828805.1 linkn.208-8564G>C intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.00000737
AC:
1
AN:
135602
Hom.:
0
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.0000282
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000737
AC:
1
AN:
135666
Hom.:
0
Cov.:
20
AF XY:
0.0000155
AC XY:
1
AN XY:
64622
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0000281
AC:
1
AN:
35550
American (AMR)
AF:
0.00
AC:
0
AN:
12404
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3386
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4246
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4190
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
7506
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
276
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
65340
Other (OTH)
AF:
0.00
AC:
0
AN:
1888
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
5075

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.48
DANN
Benign
0.23
PhyloP100
-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12119783; hg19: chr1-47855379; API